Postdoctoral Scholar in Microbiology and Bioinformatics

Institution/Company:
University of Calgary
Location:
Calgary, AB, Canada
Job Type:
  • Postdoctoral (1 year position with possibility of extension to 2 years)
Degree Level Required:
PhD
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Postdoctoral Scholar in Microbiology and Bioinformatics

Location: Foothills Campus, University of Calgary, Canada

Area: Microbiology and Bioinformatics

Duration: 1 - 2 years

Start Date: September - November 2020

Salary: Negotiable, plus benefits

Cystic fibrosis (CF) is the most common lethal genetic disease of Canadians and most of its attributable morbidity and mortality relate to repeated and eventually chronic bacterial infections involving the airways. The ultimate goal of our CF work is to understand the natural history, clinical impact and infection transmission risk of all CF-associated airways pathogens. For this work, we are actively supported by grants from CIHR, NIH, the Cystic Fibrosis Foundation, and Cystic Fibrosis Canada.

The candidate will participate in a project which involves WGS of bacterial isolates recovered from the CF airways to understand isolate relatedness between patients and the potential for patient-patient spread. Identifying factors associated with past transmission events will enable future events and their negative consequences to be avoided. Our laboratory maintains a unique resource: the Calgary Adult CF Clinic Biobank – a one-of-a-kind collection containing every bacterial pathogen isolated from CF patient from every clinical encounter (1978-present, n>55,000). Access to this one of-a-kind collection means that our group is uniquely positioned to strategically analyze bacterial infection dynamics in CF on a scale greater than any before.

The Parkins lab at the University of Calgary (https://cumming.ucalgary.ca/parkinslab/) is a translational research group and a member of the Infectious Disease Research Group.

Dr. Parkins is the Section-Chief of Infectious Diseases in the Department of Medicine, and a clinician scientist with a range of research interests pursued in his laboratory, including tracking SARS-COV2 in community wastewater, finding clinical correlates of blood stream and prosthetic joint infections, and investigating various aspects of airways infections in cystic fibrosis (CF).

We will seek to hire the most qualified applicant in the late fall of 2020/early 2021 to join a project that has already begun.

Responsibilities:

The candidate’s responsibilities will include (but are not limited to):

  • Design and manage a project from sample selection to bioinformatic data analysis
  • Collect samples and perform associated experimental work (e.g. genomic extractions, DNA sequencing library preparations, etc.) required for next-generation sequencing
  • Perform a variety of bioinformatic analyses (e.g. data cleaning, variant calling, phylogenetic and evolutionary analyses, clustering analyses)
  • Manage (update, curate, and search) sample biobank/database
  • Write, edit, and produce associated manuscripts

Qualifications:

Applicants must have a PhD in microbiology (in the last 3 years), genomics, computational biology, or related field (such as microbial evolution, population genetics, or computational biology). Applicants should have a broad microbiology background and experience with scientific computing (Python, R, Bash) and have a familiarity with working with microbial sequencing data, genomics, and phylogenetics. Prior experience with Bayesian evolutionary analyses and infection transmission dynamics is an advantage. The successful applicant should be highly motivated, have strong communication skills (verbal and written), and have a strong record of peer-reviewed publication(s) demonstrating their skills and creativity through principal authorship. The ability to work as part of a team is integral to the position.

  • How to Apply

    Please send CV and a cover letter, and/or enquiries to: Dr Michael Parkins, Director, Calgary Adult CF Clinic 3330 Hospital Drive NW, Calgary, AB T2N 4N1 email: mdparkin@ucalgary.ca